Casal2 Test Case MPD comparisons for BCO

1 BCO comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 8 Casal2 model configurations (3 BetaDiff, 2 CppAD, and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-7 vs. 2e-5).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-7 vs. 2e-5). The Casal2 CppAD models have a tolerance value of 1e-9.

1.1 BCO model characteristics

The main characteristics of the Test Case BCO (ling) CASAL model are:

• one stock, ages 3 - 20
• one area
• years 1900 - 2019, projection year 2020
• one time step
• two stock categories: male and female
• natural mortality-at-age is 0.14 for males and 0.20 for females
• sex-specific logistic maturity
• sex-specific von Bertalanffy age-length relationship
• one length-weight relationship (\(W = aL^b\))
• Beverton-Holt stock-recruitment relationship, with steepness (h) 0.75 and \(\sigma_R\) 0.6
• no ageing error
• one survey with sex-specific age-based logistic selectivity
• three fisheries, all with sex-specific length-based logistic selectivity and retained/discarded catches

Observation data include:

• survey index
• fishery CPUE index
• fishery proportions-at-length

Parameters estimated include:

• B0
• male \(L_{\infty}\)
• male age-length CV2
• sex-specific survey logistic selectivity (a50 and ato95)
• YCS (recruitment deviations)

1.2 R environment

## [1] "Mon Nov 23 15:38:54 2020"
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_GB.UTF_8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] casal2_1.0     casal_2.30     ggthemes_4.2.0 ggmcmc_1.5.0   tidyr_1.1.2   
##  [6] ggplot2_3.3.2  gridExtra_2.3  coda_0.19-4    rlist_0.4.6.1  huxtable_5.1.1
## [11] dplyr_1.0.2    plyr_1.8.6     devtools_2.3.2 usethis_1.6.3 
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.1.0   xfun_0.19          remotes_2.2.0      purrr_0.3.4       
##  [5] lattice_0.20-38    colorspace_1.4-1   vctrs_0.3.5        generics_0.1.0    
##  [9] testthat_2.3.2     htmltools_0.5.0    yaml_2.2.1         rlang_0.4.8       
## [13] pkgbuild_1.1.0     pillar_1.4.7       glue_1.4.2         withr_2.3.0       
## [17] RColorBrewer_1.1-2 sessioninfo_1.1.1  lifecycle_0.2.0    stringr_1.4.0     
## [21] munsell_0.5.0      gtable_0.3.0       memoise_1.1.0      evaluate_0.14     
## [25] GGally_1.4.0       knitr_1.30         callr_3.5.1        ps_1.4.0          
## [29] fansi_0.4.1        Rcpp_1.0.5         scales_1.1.1       desc_1.2.0        
## [33] pkgload_1.1.0      fs_1.5.0           digest_0.6.27      stringi_1.5.3     
## [37] processx_3.4.4     rprojroot_2.0.2    grid_3.6.0         cli_2.2.0         
## [41] tools_3.6.0        magrittr_2.0.1     tibble_3.0.4       crayon_1.3.4      
## [45] pkgconfig_2.0.3    ellipsis_0.3.1     data.table_1.13.2  prettyunits_1.1.1 
## [49] reshape_0.8.8      assertthat_0.2.1   rmarkdown_2.5      R6_2.5.0          
## [53] compiler_3.6.0

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')

source('../../R-functions/report_read_in_Casal2_MPD_files.R')

## Warning in sqrt(1/diag(V)): NaNs produced

## Warning in cov2cor(data): diag(.) had 0 or NA entries; non-finite result is
## doubtful

## Warning in sqrt(1/diag(V)): NaNs produced

## Warning in cov2cor(data): diag(.) had 0 or NA entries; non-finite result is
## doubtful

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates

rownames	Base_Model	Sensitivity_1	Percent_Diff
initialization.B0	14170.00000	14170.00000	0.000
recruitment.YCS1	1.00000	1.00000	0.000
recruitment.YCS2	1.00000	1.00000	0.000
recruitment.YCS3	1.00000	1.00000	0.000
recruitment.YCS4	1.00000	1.00000	0.000
recruitment.YCS5	1.00000	1.00000	0.000
recruitment.YCS6	1.00000	1.00000	0.000
recruitment.YCS7	1.00000	1.00000	0.000
recruitment.YCS8	1.00000	1.00000	0.000
recruitment.YCS9	1.00000	1.00000	0.000
recruitment.YCS10	1.00000	1.00000	0.000
recruitment.YCS11	1.00000	1.00000	0.000
recruitment.YCS12	1.00000	1.00000	0.000
recruitment.YCS13	1.00000	1.00000	0.000
recruitment.YCS14	1.00000	1.00000	0.000
recruitment.YCS15	1.00000	1.00000	0.000
recruitment.YCS16	1.00000	1.00000	0.000
recruitment.YCS17	1.00000	1.00000	0.000
recruitment.YCS18	1.00000	1.00000	0.000
recruitment.YCS19	1.00000	1.00000	0.000
recruitment.YCS20	1.00000	1.00000	0.000
recruitment.YCS21	1.00000	1.00000	0.000
recruitment.YCS22	1.00000	1.00000	0.000
recruitment.YCS23	1.00000	1.00000	0.000
recruitment.YCS24	1.00000	1.00000	0.000
recruitment.YCS25	1.00000	1.00000	0.000
recruitment.YCS26	1.00000	1.00000	0.000
recruitment.YCS27	1.00000	1.00000	0.000
recruitment.YCS28	1.00000	1.00000	0.000
recruitment.YCS29	1.00000	1.00000	0.000
recruitment.YCS30	1.00000	1.00000	0.000
recruitment.YCS31	1.00000	1.00000	0.000
recruitment.YCS32	1.00000	1.00000	0.000
recruitment.YCS33	1.00000	1.00000	0.000
recruitment.YCS34	1.00000	1.00000	0.000
recruitment.YCS35	1.00000	1.00000	0.000
recruitment.YCS36	1.00000	1.00000	0.000
recruitment.YCS37	1.00000	1.00000	0.000
recruitment.YCS38	1.00000	1.00000	0.000
recruitment.YCS39	1.00000	1.00000	0.000
recruitment.YCS40	1.00000	1.00000	0.000
recruitment.YCS41	1.00000	1.00000	0.000
recruitment.YCS42	1.00000	1.00000	0.000
recruitment.YCS43	1.00000	1.00000	0.000
recruitment.YCS44	1.00000	1.00000	0.000
recruitment.YCS45	1.00000	1.00000	0.000
recruitment.YCS46	1.00000	1.00000	0.000
recruitment.YCS47	1.00000	1.00000	0.000
recruitment.YCS48	1.00000	1.00000	0.000
recruitment.YCS49	1.00000	1.00000	0.000
recruitment.YCS50	1.00000	1.00000	0.000
recruitment.YCS51	1.00000	1.00000	0.000
recruitment.YCS52	1.00000	1.00000	0.000
recruitment.YCS53	1.00000	1.00000	0.000
recruitment.YCS54	1.00000	1.00000	0.000
recruitment.YCS55	1.00000	1.00000	0.000
recruitment.YCS56	1.00000	1.00000	0.000
recruitment.YCS57	1.00000	1.00000	0.000
recruitment.YCS58	1.00000	1.00000	0.000
recruitment.YCS59	1.00000	1.00000	0.000
recruitment.YCS60	1.00000	1.00000	0.000
recruitment.YCS61	1.00000	1.00000	0.000
recruitment.YCS62	1.00000	1.00000	0.000
recruitment.YCS63	1.00000	1.00000	0.000
recruitment.YCS64	1.00000	1.00000	0.000
recruitment.YCS65	1.00000	1.00000	0.000
recruitment.YCS66	1.00000	1.00000	0.000
recruitment.YCS67	1.00000	1.00000	0.000
recruitment.YCS68	1.00000	1.00000	0.000
recruitment.YCS69	1.00000	1.00000	0.000
recruitment.YCS70	1.00000	1.00000	0.000
recruitment.YCS71	1.00000	1.00000	0.000
recruitment.YCS72	1.00000	1.00000	0.000
recruitment.YCS73	1.00000	1.00000	0.000
recruitment.YCS74	1.00000	1.00000	0.000
recruitment.YCS75	1.00000	1.00000	0.000
recruitment.YCS76	1.00000	1.00000	0.000
recruitment.YCS77	1.00000	1.00000	0.000
recruitment.YCS78	1.00000	1.00000	0.000
recruitment.YCS79	1.00000	1.00000	0.000
recruitment.YCS80	1.00000	1.00000	0.000
recruitment.YCS81	1.00000	1.00000	0.000
recruitment.YCS82	1.00000	1.00000	0.000
recruitment.YCS83	1.00000	1.00000	0.000
recruitment.YCS84	0.23480	0.23480	0.000
recruitment.YCS85	0.23160	0.23160	0.000
recruitment.YCS86	0.23220	0.23220	0.000
recruitment.YCS87	0.24120	0.24120	0.000
recruitment.YCS88	0.26510	0.26510	0.000
recruitment.YCS89	0.31720	0.31720	0.000
recruitment.YCS90	0.42240	0.42240	0.000
recruitment.YCS91	0.61390	0.61390	0.000
recruitment.YCS92	0.92300	0.92300	0.000
recruitment.YCS93	1.42900	1.42900	0.000
recruitment.YCS94	1.48000	1.48000	0.000
recruitment.YCS95	1.00900	1.00900	0.000
recruitment.YCS96	0.84620	0.84620	0.000
recruitment.YCS97	0.85550	0.85550	0.000
recruitment.YCS98	1.08700	1.08700	0.000
recruitment.YCS99	1.53000	1.53000	0.000
recruitment.YCS100	1.02700	1.02700	0.000
recruitment.YCS101	0.79990	0.79990	0.000
recruitment.YCS102	0.82080	0.82080	0.000
recruitment.YCS103	0.63180	0.63180	0.000
recruitment.YCS104	0.80520	0.80520	0.000
recruitment.YCS105	0.74530	0.74530	0.000
recruitment.YCS106	0.46340	0.46340	0.000
recruitment.YCS107	1.07500	1.07500	0.000
recruitment.YCS108	0.89920	0.89920	0.000
recruitment.YCS109	0.38510	0.38510	0.000
recruitment.YCS110	0.91270	0.91270	0.000
recruitment.YCS111	0.70920	0.70920	0.000
recruitment.YCS112	0.82900	0.82900	0.000
recruitment.YCS113	0.42330	0.42330	0.000
recruitment.YCS114	1.27800	1.27800	0.000
recruitment.YCS115	0.68810	0.68810	0.000
recruitment.YCS116	0.74250	0.74250	0.000
recruitment.YCS117	0.57050	0.57050	0.000
recruitment.YCS118	0.45160	0.45160	0.000
recruitment.YCS119	1.00000	1.00000	0.000
recruitment.YCS120	1.00000	1.00000	0.000
size_at_age.Linf_male	47.12000	47.12000	0.000
size_at_age.cv2_male	0.06256	0.06256	0.000
selectivity[potSsel].male1	3.03900	3.03900	0.000
selectivity[potSsel].male2	0.19070	0.19060	0.052
selectivity[potSsel].female1	3.31600	3.31600	0.000
selectivity[potSsel].female2	1.04500	1.04500	0.000

Casal2 parameter estimates

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	cppad_casal_flags_on	cppad_casal_flags_off	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	14199.60000	14210.70000	14199.60000	14199.60000	14210.70000	14199.60000	14210.70000	14199.60000
age_length[asMm0].linf	47.33060	47.31350	47.33060	47.33060	47.31350	47.33060	47.31350	47.33060
age_length[asMm0].cv_last	0.05978	0.06142	0.05978	0.05978	0.06142	0.05978	0.06142	0.05978
selectivity[potSurveySel_male].a50	3.03935	3.04011	3.03932	3.03959	3.04015	3.03935	3.04011	3.03932
selectivity[potSurveySel_male].ato95	0.19078	0.19176	0.19062	0.19191	0.19197	0.19078	0.19176	0.19062
selectivity[potSurveySel_female].a50	3.31449	3.31509	3.31450	3.31450	3.31510	3.31449	3.31509	3.31450
selectivity[potSurveySel_female].ato95	1.03324	1.02647	1.03325	1.03325	1.02651	1.03324	1.02647	1.03325
process[Recruitment].ycs_values{1980}	0.23522	0.23512	0.23522	0.23522	0.23512	0.23522	0.23512	0.23522
process[Recruitment].ycs_values{1981}	0.23218	0.23209	0.23218	0.23218	0.23209	0.23218	0.23209	0.23218
process[Recruitment].ycs_values{1982}	0.23321	0.23317	0.23321	0.23321	0.23317	0.23321	0.23317	0.23321
process[Recruitment].ycs_values{1983}	0.24199	0.24199	0.24199	0.24199	0.24199	0.24199	0.24199	0.24199
process[Recruitment].ycs_values{1984}	0.26464	0.26470	0.26464	0.26464	0.26470	0.26464	0.26470	0.26464
process[Recruitment].ycs_values{1985}	0.31484	0.31495	0.31484	0.31484	0.31495	0.31484	0.31495	0.31484
process[Recruitment].ycs_values{1986}	0.41617	0.41635	0.41617	0.41617	0.41635	0.41617	0.41635	0.41617
process[Recruitment].ycs_values{1987}	0.60174	0.60199	0.60174	0.60174	0.60200	0.60174	0.60199	0.60174
process[Recruitment].ycs_values{1988}	0.90212	0.90257	0.90212	0.90212	0.90255	0.90212	0.90257	0.90212
process[Recruitment].ycs_values{1989}	1.37833	1.37987	1.37833	1.37833	1.37986	1.37833	1.37987	1.37833
process[Recruitment].ycs_values{1990}	1.56002	1.55856	1.56001	1.56001	1.55858	1.56002	1.55856	1.56001
process[Recruitment].ycs_values{1991}	1.02890	1.02850	1.02891	1.02891	1.02851	1.02890	1.02850	1.02891
process[Recruitment].ycs_values{1992}	0.84788	0.84782	0.84788	0.84788	0.84780	0.84788	0.84782	0.84788
process[Recruitment].ycs_values{1993}	0.84686	0.84708	0.84685	0.84685	0.84708	0.84686	0.84708	0.84685
process[Recruitment].ycs_values{1994}	1.06536	1.06575	1.06536	1.06536	1.06575	1.06536	1.06575	1.06536
process[Recruitment].ycs_values{1995}	1.54897	1.54805	1.54897	1.54897	1.54810	1.54897	1.54805	1.54897
process[Recruitment].ycs_values{1996}	1.05329	1.05345	1.05327	1.05327	1.05337	1.05329	1.05345	1.05327
process[Recruitment].ycs_values{1997}	0.80305	0.80290	0.80306	0.80306	0.80294	0.80305	0.80290	0.80306
process[Recruitment].ycs_values{1998}	0.81669	0.81658	0.81669	0.81669	0.81658	0.81669	0.81658	0.81669
process[Recruitment].ycs_values{1999}	0.62838	0.62894	0.62838	0.62838	0.62894	0.62838	0.62894	0.62838
process[Recruitment].ycs_values{2000}	0.80206	0.80234	0.80206	0.80206	0.80234	0.80206	0.80234	0.80206
process[Recruitment].ycs_values{2001}	0.74581	0.74599	0.74581	0.74581	0.74599	0.74581	0.74599	0.74581
process[Recruitment].ycs_values{2002}	0.46713	0.46675	0.46713	0.46713	0.46675	0.46713	0.46675	0.46713
process[Recruitment].ycs_values{2003}	1.09423	1.09063	1.09423	1.09423	1.09063	1.09423	1.09063	1.09423
process[Recruitment].ycs_values{2004}	0.92128	0.91711	0.92128	0.92128	0.91710	0.92128	0.91711	0.92128
process[Recruitment].ycs_values{2005}	0.38413	0.38256	0.38413	0.38413	0.38256	0.38413	0.38256	0.38413
process[Recruitment].ycs_values{2006}	0.90589	0.90190	0.90589	0.90589	0.90190	0.90589	0.90190	0.90589
process[Recruitment].ycs_values{2007}	0.70981	0.72045	0.70981	0.70981	0.72045	0.70981	0.72045	0.70981
process[Recruitment].ycs_values{2008}	0.83557	0.83479	0.83557	0.83557	0.83479	0.83557	0.83479	0.83557
process[Recruitment].ycs_values{2009}	0.42630	0.42606	0.42629	0.42630	0.42606	0.42630	0.42606	0.42629
process[Recruitment].ycs_values{2010}	1.28746	1.28707	1.28746	1.28746	1.28707	1.28746	1.28707	1.28746
process[Recruitment].ycs_values{2011}	0.69033	0.69110	0.69033	0.69033	0.69110	0.69033	0.69110	0.69033
process[Recruitment].ycs_values{2012}	0.73638	0.73678	0.73638	0.73638	0.73678	0.73638	0.73678	0.73638
process[Recruitment].ycs_values{2013}	0.56156	0.56190	0.56156	0.56156	0.56190	0.56156	0.56190	0.56156
process[Recruitment].ycs_values{2014}	0.43978	0.43978	0.43978	0.43978	0.43978	0.43978	0.43978	0.43978

Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	cppad_casal_flags_on	cppad_casal_flags_off	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	0.000	-0.078	0.000	0.000	-0.078	0.000	-0.078	0.000
age_length[asMm0].linf	0.000	0.036	0.000	0.000	0.036	0.000	0.036	0.000
age_length[asMm0].cv_last	0.000	-2.757	0.000	0.000	-2.757	0.000	-2.757	0.000
selectivity[potSurveySel_male].a50	0.000	-0.025	0.001	-0.008	-0.026	0.000	-0.025	0.001
selectivity[potSurveySel_male].ato95	0.000	-0.518	0.084	-0.594	-0.626	0.000	-0.518	0.084
selectivity[potSurveySel_female].a50	0.000	-0.018	-0.000	-0.000	-0.018	0.000	-0.018	-0.000
selectivity[potSurveySel_female].ato95	0.000	0.655	-0.001	-0.001	0.651	0.000	0.655	-0.001
process[Recruitment].ycs_values{1980}	0.000	0.045	0.000	0.000	0.045	0.000	0.045	0.000
process[Recruitment].ycs_values{1981}	0.000	0.037	0.000	0.000	0.037	0.000	0.037	0.000
process[Recruitment].ycs_values{1982}	0.000	0.019	0.000	0.000	0.019	0.000	0.019	0.000
process[Recruitment].ycs_values{1983}	0.000	-0.002	0.000	-0.000	-0.002	0.000	-0.002	0.000
process[Recruitment].ycs_values{1984}	0.000	-0.021	0.000	0.000	-0.021	0.000	-0.021	0.000
process[Recruitment].ycs_values{1985}	0.000	-0.035	0.000	0.000	-0.036	0.000	-0.035	0.000
process[Recruitment].ycs_values{1986}	0.000	-0.042	0.000	0.000	-0.042	0.000	-0.042	0.000
process[Recruitment].ycs_values{1987}	0.000	-0.042	-0.000	-0.000	-0.043	0.000	-0.042	-0.000
process[Recruitment].ycs_values{1988}	0.000	-0.049	0.001	0.001	-0.047	0.000	-0.049	0.001
process[Recruitment].ycs_values{1989}	0.000	-0.112	0.000	0.000	-0.111	0.000	-0.112	0.000
process[Recruitment].ycs_values{1990}	0.000	0.094	0.001	0.001	0.092	0.000	0.094	0.001
process[Recruitment].ycs_values{1991}	0.000	0.039	-0.001	-0.001	0.038	0.000	0.039	-0.001
process[Recruitment].ycs_values{1992}	0.000	0.007	0.000	0.000	0.009	0.000	0.007	0.000
process[Recruitment].ycs_values{1993}	0.000	-0.027	0.001	0.001	-0.026	0.000	-0.027	0.001
process[Recruitment].ycs_values{1994}	0.000	-0.037	0.000	0.000	-0.037	0.000	-0.037	0.000
process[Recruitment].ycs_values{1995}	0.000	0.059	0.000	0.000	0.056	0.000	0.059	0.000
process[Recruitment].ycs_values{1996}	0.000	-0.015	0.002	0.002	-0.008	0.000	-0.015	0.002
process[Recruitment].ycs_values{1997}	0.000	0.018	-0.001	-0.001	0.015	0.000	0.018	-0.001
process[Recruitment].ycs_values{1998}	0.000	0.014	-0.000	-0.000	0.013	0.000	0.014	-0.000
process[Recruitment].ycs_values{1999}	0.000	-0.089	0.000	0.000	-0.089	0.000	-0.089	0.000
process[Recruitment].ycs_values{2000}	0.000	-0.035	0.000	0.000	-0.034	0.000	-0.035	0.000
process[Recruitment].ycs_values{2001}	0.000	-0.024	0.000	0.000	-0.024	0.000	-0.024	0.000
process[Recruitment].ycs_values{2002}	0.000	0.080	0.000	0.000	0.080	0.000	0.080	0.000
process[Recruitment].ycs_values{2003}	0.000	0.329	0.000	0.000	0.329	0.000	0.329	0.000
process[Recruitment].ycs_values{2004}	0.000	0.453	0.000	0.000	0.453	0.000	0.453	0.000
process[Recruitment].ycs_values{2005}	0.000	0.408	0.000	0.000	0.408	0.000	0.408	0.000
process[Recruitment].ycs_values{2006}	0.000	0.440	0.000	0.000	0.440	0.000	0.440	0.000
process[Recruitment].ycs_values{2007}	0.000	-1.499	0.000	0.000	-1.499	0.000	-1.499	0.000
process[Recruitment].ycs_values{2008}	0.000	0.093	0.000	0.000	0.093	0.000	0.093	0.000
process[Recruitment].ycs_values{2009}	0.000	0.054	0.000	0.000	0.054	0.000	0.054	0.000
process[Recruitment].ycs_values{2010}	0.000	0.030	0.000	0.000	0.030	0.000	0.030	0.000
process[Recruitment].ycs_values{2011}	0.000	-0.111	0.000	0.000	-0.111	0.000	-0.111	0.000
process[Recruitment].ycs_values{2012}	0.000	-0.054	0.000	0.000	-0.054	0.000	-0.054	0.000
process[Recruitment].ycs_values{2013}	0.000	-0.062	0.000	0.000	-0.062	0.000	-0.062	0.000
process[Recruitment].ycs_values{2014}	0.000	0.001	0.000	0.000	0.001	0.000	0.001	0.000

CASAL objective function component values

Component	Base_Model	Sensitivity_1
potCPUE	-51.180	-51.180
potSurveyAbd	-3.254	-3.254
logbookLF	54.660	54.660
potCommAF	54.410	54.410
potSurveyAF	118.200	118.200
recCatchLF	68.040	68.040
prior_on_initialization.B0	9.559	9.559
prior_on_recruitment.YCS	9.658	9.658
prior_on_size_at_age.Linf_male	0.000	0.000
prior_on_size_at_age.cv2_male	0.000	0.000
prior_on_selectivity[potSsel].male	0.000	0.000
prior_on_selectivity[potSsel].female	0.000	0.000
prior_on_q_qPotCPUE	-8.331	-8.331
prior_on_q_potSurveyq	-11.380	-11.380
clp1F	0.000	0.000
clp2F	0.000	0.000
clp3F	0.000	0.000
YCS	0.566	0.566
Total	241.000	241.000

Casal2 objective function component values

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	cppad_casal_flags_on	cppad_casal_flags_off	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
observation->potSurvey-2010	-1.038	-1.042	-1.038	-1.038	-1.042	-1.038	-1.042	-1.038
observation->potSurvey-2014	-1.020	-1.022	-1.020	-1.020	-1.022	-1.020	-1.022	-1.020
observation->potSurvey-2018	-1.196	-1.197	-1.196	-1.196	-1.197	-1.196	-1.197	-1.196
observation->potCPUE-1990	-0.162	-0.159	-0.162	-0.162	-0.159	-0.162	-0.159	-0.162
observation->potCPUE-1991	1.098	1.102	1.098	1.098	1.102	1.098	1.102	1.098
observation->potCPUE-1992	-1.057	-1.053	-1.057	-1.057	-1.053	-1.057	-1.053	-1.057
observation->potCPUE-1993	-1.991	-1.990	-1.991	-1.991	-1.990	-1.991	-1.990	-1.991
observation->potCPUE-1994	-2.144	-2.143	-2.144	-2.144	-2.143	-2.144	-2.143	-2.144
observation->potCPUE-1995	-2.085	-2.085	-2.085	-2.085	-2.085	-2.085	-2.085	-2.085
observation->potCPUE-1996	-2.186	-2.186	-2.186	-2.186	-2.186	-2.186	-2.186	-2.186
observation->potCPUE-1997	-1.960	-1.959	-1.960	-1.960	-1.959	-1.960	-1.959	-1.960
observation->potCPUE-1998	-2.157	-2.157	-2.157	-2.157	-2.157	-2.157	-2.157	-2.157
observation->potCPUE-1999	-1.689	-1.689	-1.689	-1.689	-1.689	-1.689	-1.689	-1.689
observation->potCPUE-2000	-2.192	-2.192	-2.192	-2.192	-2.192	-2.192	-2.192	-2.192
observation->potCPUE-2001	-2.164	-2.164	-2.164	-2.164	-2.164	-2.164	-2.164	-2.164
observation->potCPUE-2002	-2.042	-2.042	-2.042	-2.042	-2.042	-2.042	-2.042	-2.042
observation->potCPUE-2003	-2.172	-2.173	-2.172	-2.172	-2.173	-2.172	-2.173	-2.172
observation->potCPUE-2004	-2.192	-2.192	-2.192	-2.192	-2.192	-2.192	-2.192	-2.192
observation->potCPUE-2005	-1.908	-1.911	-1.908	-1.908	-1.911	-1.908	-1.911	-1.908
observation->potCPUE-2006	-1.793	-1.797	-1.793	-1.793	-1.797	-1.793	-1.797	-1.793
observation->potCPUE-2007	-2.176	-2.177	-2.176	-2.176	-2.177	-2.176	-2.177	-2.176
observation->potCPUE-2008	-2.188	-2.189	-2.188	-2.188	-2.189	-2.188	-2.189	-2.188
observation->potCPUE-2009	-2.051	-2.051	-2.051	-2.051	-2.051	-2.051	-2.051	-2.051
observation->potCPUE-2010	-2.122	-2.124	-2.122	-2.122	-2.124	-2.122	-2.124	-2.122
observation->potCPUE-2011	-1.875	-1.865	-1.875	-1.875	-1.865	-1.875	-1.865	-1.875
observation->potCPUE-2012	-1.767	-1.756	-1.767	-1.767	-1.756	-1.767	-1.756	-1.767
observation->potCPUE-2013	-1.775	-1.769	-1.775	-1.775	-1.769	-1.775	-1.769	-1.775
observation->potCPUE-2014	-1.038	-1.034	-1.038	-1.038	-1.034	-1.038	-1.034	-1.038
observation->potCPUE-2015	-1.851	-1.851	-1.851	-1.851	-1.851	-1.851	-1.851	-1.851
observation->potCPUE-2016	-2.092	-2.092	-2.092	-2.092	-2.092	-2.092	-2.092	-2.092
observation->potCPUE-2017	-2.104	-2.105	-2.104	-2.104	-2.105	-2.104	-2.105	-2.104
observation->potCPUE-2018	-1.352	-1.347	-1.352	-1.352	-1.347	-1.352	-1.347	-1.352
observation->AFpotSurvey-2010	39.659	39.754	39.659	39.659	39.754	39.659	39.754	39.659
observation->AFpotSurvey-2014	39.371	39.383	39.371	39.371	39.383	39.371	39.383	39.371
observation->AFpotSurvey-2018	39.165	39.136	39.165	39.165	39.136	39.165	39.136	39.165
observation->AFpotFishing-2018	47.103	47.146	47.103	47.103	47.146	47.103	47.146	47.103
observation->AFpotFishing-2019	7.888	7.887	7.888	7.888	7.887	7.888	7.887	7.888
observation->lgobookLF	54.894	54.862	54.894	54.894	54.862	54.894	54.862	54.894
observation->rec.catch.LF	67.727	68.611	67.727	67.727	68.611	67.727	68.611	67.727
prior->B0->process[Recruitment].b0	9.561	9.562	9.561	9.561	9.562	9.561	9.562	9.561
prior->male_Linf->age_length[asMm0].linf	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->male_cv2->age_length[asMm0].cv_last	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_mA50->selectivity[potSurveySel_male].a50	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_mAto95->selectivity[potSurveySel_male].ato95	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_fA50->selectivity[potSurveySel_female].a50	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_fAto95->selectivity[potSurveySel_female].ato95	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->YCS->process[Recruitment].ycs_values{1980}	1.273	1.275	1.273	1.273	1.275	1.273	1.275	1.273
prior->YCS->process[Recruitment].ycs_values{1981}	1.315	1.317	1.315	1.315	1.317	1.315	1.317	1.315
prior->YCS->process[Recruitment].ycs_values{1982}	1.301	1.302	1.301	1.301	1.302	1.301	1.302	1.301
prior->YCS->process[Recruitment].ycs_values{1983}	1.184	1.184	1.184	1.184	1.184	1.184	1.184	1.184
prior->YCS->process[Recruitment].ycs_values{1984}	0.918	0.917	0.918	0.918	0.917	0.918	0.917	0.918
prior->YCS->process[Recruitment].ycs_values{1985}	0.477	0.476	0.477	0.477	0.476	0.477	0.476	0.477
prior->YCS->process[Recruitment].ycs_values{1986}	-0.027	-0.027	-0.027	-0.027	-0.027	-0.027	-0.027	-0.027
prior->YCS->process[Recruitment].ycs_values{1987}	-0.304	-0.304	-0.304	-0.304	-0.304	-0.304	-0.304	-0.304
prior->YCS->process[Recruitment].ycs_values{1988}	-0.099	-0.098	-0.099	-0.099	-0.098	-0.099	-0.098	-0.099
prior->YCS->process[Recruitment].ycs_values{1989}	0.687	0.690	0.687	0.687	0.690	0.687	0.690	0.687
prior->YCS->process[Recruitment].ycs_values{1990}	1.027	1.024	1.027	1.027	1.024	1.027	1.024	1.027
prior->YCS->process[Recruitment].ycs_values{1991}	0.082	0.082	0.083	0.083	0.082	0.082	0.082	0.083
prior->YCS->process[Recruitment].ycs_values{1992}	-0.165	-0.165	-0.165	-0.165	-0.165	-0.165	-0.165	-0.165
prior->YCS->process[Recruitment].ycs_values{1993}	-0.166	-0.166	-0.166	-0.166	-0.166	-0.166	-0.166	-0.166
prior->YCS->process[Recruitment].ycs_values{1994}	0.140	0.141	0.140	0.140	0.141	0.140	0.141	0.140
prior->YCS->process[Recruitment].ycs_values{1995}	1.006	1.004	1.006	1.006	1.005	1.006	1.004	1.006
prior->YCS->process[Recruitment].ycs_values{1996}	0.121	0.121	0.121	0.121	0.121	0.121	0.121	0.121
prior->YCS->process[Recruitment].ycs_values{1997}	-0.212	-0.212	-0.212	-0.212	-0.212	-0.212	-0.212	-0.212
prior->YCS->process[Recruitment].ycs_values{1998}	-0.199	-0.199	-0.199	-0.199	-0.199	-0.199	-0.199	-0.199
prior->YCS->process[Recruitment].ycs_values{1999}	-0.307	-0.307	-0.307	-0.307	-0.307	-0.307	-0.307	-0.307
prior->YCS->process[Recruitment].ycs_values{2000}	-0.213	-0.213	-0.213	-0.213	-0.213	-0.213	-0.213	-0.213
prior->YCS->process[Recruitment].ycs_values{2001}	-0.262	-0.261	-0.262	-0.262	-0.261	-0.262	-0.261	-0.262
prior->YCS->process[Recruitment].ycs_values{2002}	-0.161	-0.160	-0.161	-0.161	-0.160	-0.161	-0.160	-0.161
prior->YCS->process[Recruitment].ycs_values{2003}	0.187	0.181	0.187	0.187	0.181	0.187	0.181	0.187
prior->YCS->process[Recruitment].ycs_values{2004}	-0.074	-0.079	-0.074	-0.074	-0.079	-0.074	-0.079	-0.074
prior->YCS->process[Recruitment].ycs_values{2005}	0.092	0.098	0.092	0.092	0.098	0.092	0.098	0.092
prior->YCS->process[Recruitment].ycs_values{2006}	-0.094	-0.099	-0.094	-0.094	-0.099	-0.094	-0.099	-0.094
prior->YCS->process[Recruitment].ycs_values{2007}	-0.285	-0.279	-0.285	-0.285	-0.279	-0.285	-0.279	-0.285
prior->YCS->process[Recruitment].ycs_values{2008}	-0.179	-0.179	-0.179	-0.179	-0.179	-0.179	-0.179	-0.179
prior->YCS->process[Recruitment].ycs_values{2009}	-0.058	-0.058	-0.058	-0.058	-0.058	-0.058	-0.058	-0.058
prior->YCS->process[Recruitment].ycs_values{2010}	0.521	0.521	0.521	0.521	0.521	0.521	0.521	0.521
prior->YCS->process[Recruitment].ycs_values{2011}	-0.294	-0.294	-0.294	-0.294	-0.294	-0.294	-0.294	-0.294
prior->YCS->process[Recruitment].ycs_values{2012}	-0.268	-0.268	-0.268	-0.268	-0.268	-0.268	-0.268	-0.268
prior->YCS->process[Recruitment].ycs_values{2013}	-0.286	-0.286	-0.286	-0.286	-0.286	-0.286	-0.286	-0.286
prior->YCS->process[Recruitment].ycs_values{2014}	-0.096	-0.096	-0.096	-0.096	-0.096	-0.096	-0.096	-0.096
additional_prior->PrSurveyQ	-11.367	-11.368	-11.367	-11.367	-11.368	-11.367	-11.368	-11.367
additional_prior->PrCPUEQ	-8.333	-8.334	-8.333	-8.333	-8.334	-8.333	-8.334	-8.333
additional_prior->YCS_average_1	0.559	0.559	0.559	0.559	0.559	0.559	0.559	0.559
total_negloglike	238.370	239.365	238.370	238.370	239.365	238.370	239.365	238.370

## [1] "CASAL base model convergence information"
## [1] "Minimiser convergence threshold: 2e-005"                                                                 
## [2] "fmm: have converged: t = 1.53773e-005 f = 240.986"                                                       
## [3] "Successful convergence in optimise"                                                                      
## [4] "Minimiser achieved convergence after 91 quasi-Newton iterations using 101 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-007"                                                                                 
## [2] "fmm: step size too small. Indicates successful convergence (though this is not the textbook ideal convergence situation)"
## [3] "Successful convergence in optimise"                                                                                      
## [4] "Minimiser achieved convergence after 99 quasi-Newton iterations using 119 objective function evaluations"                
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 4.14863e-06 f = 238.37"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 2.71219e-06 f = 239.365"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: step size too small. Indicates successful convergence (though this is not the textbook ideal convergence situation)"
## [2] "Successful convergence in optimise"                                                                                      
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       42"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:      903"
##  [4] "Number of Iterations....: 20"                                   
##  [5] "Number of objective function evaluations             = 110"     
##  [6] "Number of objective gradient evaluations             = 21"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 110"     
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 21"      
## [11] "Number of Lagrangian Hessian evaluations             = 20"      
## [12] "EXIT: Maximum Number of Iterations Exceeded."                   
## [13] "Number of nonzeros in equality constraint Jacobian...:        0"
## [14] "Number of nonzeros in inequality constraint Jacobian.:       42"
## [15] "Number of nonzeros in Lagrangian Hessian.............:      903"
## [16] "Number of Iterations....: 20"                                   
## [17] "Number of objective function evaluations             = 146"     
## [18] "Number of objective gradient evaluations             = 21"      
## [19] "Number of equality constraint evaluations            = 0"       
## [20] "Number of inequality constraint evaluations          = 146"     
## [21] "Number of equality constraint Jacobian evaluations   = 0"       
## [22] "Number of inequality constraint Jacobian evaluations = 21"      
## [23] "Number of Lagrangian Hessian evaluations             = 20"      
## [24] "EXIT: Maximum Number of Iterations Exceeded."                   
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       42"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:      903"
##  [4] "Number of Iterations....: 20"                                   
##  [5] "Number of objective function evaluations             = 115"     
##  [6] "Number of objective gradient evaluations             = 21"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 115"     
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 21"      
## [11] "Number of Lagrangian Hessian evaluations             = 20"      
## [12] "EXIT: Maximum Number of Iterations Exceeded."                   
## [13] "Number of nonzeros in equality constraint Jacobian...:        0"
## [14] "Number of nonzeros in inequality constraint Jacobian.:       42"
## [15] "Number of nonzeros in Lagrangian Hessian.............:      903"
## [16] "Number of Iterations....: 20"                                   
## [17] "Number of objective function evaluations             = 154"     
## [18] "Number of objective gradient evaluations             = 21"      
## [19] "Number of equality constraint evaluations            = 0"       
## [20] "Number of inequality constraint evaluations          = 154"     
## [21] "Number of equality constraint Jacobian evaluations   = 0"       
## [22] "Number of inequality constraint Jacobian evaluations = 21"      
## [23] "Number of Lagrangian Hessian evaluations             = 20"      
## [24] "EXIT: Maximum Number of Iterations Exceeded."                   
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)

## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## 
## $type
## [1] "warnings"

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_on"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_off"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others...

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.6876 0.9999"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.6894 0.9999"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.704685923556288 0.999820714207084"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.697745743037247 0.999864061627529"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.719268887862089 0.999845946100166"

## [1] "Casal2 cppad_casal_flags_on parameter correlation range (excluding 1.0): -0.708287635061791 0.678193985161796"

## [1] "Casal2 cppad_casal_flags_off parameter correlation range (excluding 1.0): -0.705974195067 0.685973588521794"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.704683609734695 0.99981954195823"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.697745743037247 0.999863100354264"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.719263523071944 0.999846316745602"